problem 3

edevog · Nov 4, 2015 · 8036944 · 8036944
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diff --git a/week10/02-fasta-search.pl b/week10/02-fasta-search.pl
@@ -3,7 +3,7 @@
 use strict;
 use warnings;
 use autodie;
-use Bio::DB::Fasta'get_all_primary_ids';
+use Bio::DB::Fasta 'get_all_primary_ids';
 use Bio::SeqIO;
 use feature 'say';
 use Getopt::Long;

diff --git a/week10/03-find-cds.pl b/week10/03-find-cds.pl
@@ -0,0 +1,107 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use autodie;
+use Bio::Seq;
+use Bio::SeqIO;
+use feature 'say';
+use Getopt::Long;
+use Pod::Usage;
+
+my %opts = get_opts();
+my @args = @ARGV;
+
+if ($opts{'help'} || $opts{'man'}) {
+    pod2usage({
+        -exitval => 0,
+        -verbose => $opts{'man'} ? 2 : 1
+    });
+}
+
+for my $file (@ARGV) {
+    my $in = Bio::SeqIO->new(-file   => $file,
+                             -format => 'Genbank');
+
+#    while (my $seq = $in->next_seq){
+#        for my $feat_object ($seq->get_SeqFeatures) {          
+#           print "primary tag: ", $feat_object->primary_tag, "\n";          
+#           for my $tag ($feat_object->get_all_tags) {             
+#              print "  tag: ", $tag, "\n";             
+#              for my $value ($feat_object->get_tag_values($tag)) {                
+#                 print "    value: ", $value, "\n";             
+#              }          
+#           }       
+#        }
+#    }
+my $count = 0;
+    while (my $seq = $in->next_seq){
+        my @cds = grep { $_->primary_tag eq 'CDS' } $seq->top_SeqFeatures;
+        #say Dumper(\@cds); use Data::Dumper;
+        $count++; 
+        my $seq_id = $seq->id;
+        my $ncds   = scalar @cds;
+        say "$seq_id has $ncds CDS";
+        my $i; 
+        for my $cds (@cds) {
+            say ++$i, ": ", $cds->get_tag_values('translation');
+        }
+    }
+}
+say "OK";
+
+# --------------------------------------------------
+sub get_opts {
+    my %opts;
+    GetOptions(
+        \%opts,
+        'help',
+        'man',
+    ) or pod2usage(2);
+
+    return %opts;
+}
+
+__END__
+
+# --------------------------------------------------
+
+=pod
+
+=head1 NAME
+
+03-find-cds.pl - problem 3
+
+=head1 SYNOPSIS
+
+Usage:
+      03-find-cds.pl rec.gb [rec2.gb ...]
+
+Options:
+
+  --help   Show brief help and exit
+  --man    Show full documentation
+
+=head1 DESCRIPTION
+
+Prints the coding regions (CDSs) of the genbank records. The script can handle multiple input files, multiple sequence per file and multiple CDSs per sequence.
+
+=head1 SEE ALSO
+
+perl.
+
+=head1 AUTHOR
+
+Beth De Vogelaere E<lt>edevog@email.arizona.eduE<gt>.
+
+=head1 COPYRIGHT
+
+Copyright (c) 2015 Beth De Vogelaere
+
+This module is free software; you can redistribute it and/or
+modify it under the terms of the GPL (either version 1, or at
+your option, any later version) or the Artistic License 2.0.
+Refer to LICENSE for the full license text and to DISCLAIMER for
+additional warranty disclaimers.
+
+=cut
diff --git a/week10/ncbi-sample-rec.gb b/week10/ncbi-sample-rec.gb
@@ -0,0 +1,165 @@
+LOCUS       SCU49845     5028 bp    DNA             PLN       21-JUN-1999
+DEFINITION  Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p
+            (AXL2) and Rev7p (REV7) genes, complete cds.
+ACCESSION   U49845
+VERSION     U49845.1  GI:1293613
+KEYWORDS    .
+SOURCE      Saccharomyces cerevisiae (baker's yeast)
+  ORGANISM  Saccharomyces cerevisiae
+            Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;
+            Saccharomycetales; Saccharomycetaceae; Saccharomyces.
+REFERENCE   1  (bases 1 to 5028)
+  AUTHORS   Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W.
+  TITLE     Cloning and sequence of REV7, a gene whose function is required for
+            DNA damage-induced mutagenesis in Saccharomyces cerevisiae
+  JOURNAL   Yeast 10 (11), 1503-1509 (1994)
+  PUBMED    7871890
+REFERENCE   2  (bases 1 to 5028)
+  AUTHORS   Roemer,T., Madden,K., Chang,J. and Snyder,M.
+  TITLE     Selection of axial growth sites in yeast requires Axl2p, a novel
+            plasma membrane glycoprotein
+  JOURNAL   Genes Dev. 10 (7), 777-793 (1996)
+  PUBMED    8846915
+REFERENCE   3  (bases 1 to 5028)
+  AUTHORS   Roemer,T.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, New
+            Haven, CT, USA
+FEATURES             Location/Qualifiers
+     source          1..5028
+                     /organism="Saccharomyces cerevisiae"
+                     /db_xref="taxon:4932"
+                     /chromosome="IX"
+                     /map="9"
+     CDS             <1..206
+                     /codon_start=3
+                     /product="TCP1-beta"
+                     /protein_id="AAA98665.1"
+                     /db_xref="GI:1293614"
+                     /translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA
+                     AEVLLRVDNIIRARPRTANRQHM"
+     gene            687..3158
+                     /gene="AXL2"
+     CDS             687..3158
+                     /gene="AXL2"
+                     /note="plasma membrane glycoprotein"
+                     /codon_start=1
+                     /function="required for axial budding pattern of S.
+                     cerevisiae"
+                     /product="Axl2p"
+                     /protein_id="AAA98666.1"
+                     /db_xref="GI:1293615"
+                     /translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESF
+                     TFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFN
+                     VILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNE
+                     VFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPE
+                     TSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYV
+                     YLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYG
+                     DVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQ
+                     DHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSA
+                     NATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIA
+                     CGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLN
+                     NPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQ
+                     SQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDS
+                     YGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTK
+                     HRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRL
+                     VDFSNKSNVNVGQVKDIHGRIPEML"
+     gene            complement(3300..4037)
+                     /gene="REV7"
+     CDS             complement(3300..4037)
+                     /gene="REV7"
+                     /codon_start=1
+                     /product="Rev7p"
+                     /protein_id="AAA98667.1"
+                     /db_xref="GI:1293616"
+                     /translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ
+                     FVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVD
+                     KDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNR
+                     RVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEK
+                     LISGDDKILNGVYSQYEEGESIFGSLF"
+ORIGIN
+        1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg
+       61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct
+      121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa
+      181 gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa taataaaccg
+      241 ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta tataattcaa
+      301 agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg tcacaaataa
+      361 attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca agaatgtaat
+      421 aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc tccttgccga
+      481 gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat tttcttattc
+      541 tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta gaagaacaga
+      601 acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt ccaacatcta
+      661 cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta ttgctgacag
+      721 ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat cctatcggaa
+      781 aacaataccc cccagtggca agagtcaatg aatcgtttac atttcaaatt tccaatgata
+      841 cctataaatc gtctgtagac aagacagctc aaataacata caattgcttc gacttaccga
+      901 gctggctttc gtttgactct agttctagaa cgttctcagg tgaaccttct tctgacttac
+      961 tatctgatgc gaacaccacg ttgtatttca atgtaatact cgagggtacg gactctgccg
+     1021 acagcacgtc tttgaacaat acataccaat ttgttgttac aaaccgtcca tccatctcgc
+     1081 tatcgtcaga tttcaatcta ttggcgttgt taaaaaacta tggttatact aacggcaaaa
+     1141 acgctctgaa actagatcct aatgaagtct tcaacgtgac ttttgaccgt tcaatgttca
+     1201 ctaacgaaga atccattgtg tcgtattacg gacgttctca gttgtataat gcgccgttac
+     1261 ccaattggct gttcttcgat tctggcgagt tgaagtttac tgggacggca ccggtgataa
+     1321 actcggcgat tgctccagaa acaagctaca gttttgtcat catcgctaca gacattgaag
+     1381 gattttctgc cgttgaggta gaattcgaat tagtcatcgg ggctcaccag ttaactacct
+     1441 ctattcaaaa tagtttgata atcaacgtta ctgacacagg taacgtttca tatgacttac
+     1501 ctctaaacta tgtttatctc gatgacgatc ctatttcttc tgataaattg ggttctataa
+     1561 acttattgga tgctccagac tgggtggcat tagataatgc taccatttcc gggtctgtcc
+     1621 cagatgaatt actcggtaag aactccaatc ctgccaattt ttctgtgtcc atttatgata
+     1681 cttatggtga tgtgatttat ttcaacttcg aagttgtctc cacaacggat ttgtttgcca
+     1741 ttagttctct tcccaatatt aacgctacaa ggggtgaatg gttctcctac tattttttgc
+     1801 cttctcagtt tacagactac gtgaatacaa acgtttcatt agagtttact aattcaagcc
+     1861 aagaccatga ctgggtgaaa ttccaatcat ctaatttaac attagctgga gaagtgccca
+     1921 agaatttcga caagctttca ttaggtttga aagcgaacca aggttcacaa tctcaagagc
+     1981 tatattttaa catcattggc atggattcaa agataactca ctcaaaccac agtgcgaatg
+     2041 caacgtccac aagaagttct caccactcca cctcaacaag ttcttacaca tcttctactt
+     2101 acactgcaaa aatttcttct acctccgctg ctgctacttc ttctgctcca gcagcgctgc
+     2161 cagcagccaa taaaacttca tctcacaata aaaaagcagt agcaattgcg tgcggtgttg
+     2221 ctatcccatt aggcgttatc ctagtagctc tcatttgctt cctaatattc tggagacgca
+     2281 gaagggaaaa tccagacgat gaaaacttac cgcatgctat tagtggacct gatttgaata
+     2341 atcctgcaaa taaaccaaat caagaaaacg ctacaccttt gaacaacccc tttgatgatg
+     2401 atgcttcctc gtacgatgat acttcaatag caagaagatt ggctgctttg aacactttga
+     2461 aattggataa ccactctgcc actgaatctg atatttccag cgtggatgaa aagagagatt
+     2521 ctctatcagg tatgaataca tacaatgatc agttccaatc ccaaagtaaa gaagaattat
+     2581 tagcaaaacc cccagtacag cctccagaga gcccgttctt tgacccacag aataggtctt
+     2641 cttctgtgta tatggatagt gaaccagcag taaataaatc ctggcgatat actggcaacc
+     2701 tgtcaccagt ctctgatatt gtcagagaca gttacggatc acaaaaaact gttgatacag
+     2761 aaaaactttt cgatttagaa gcaccagaga aggaaaaacg tacgtcaagg gatgtcacta
+     2821 tgtcttcact ggacccttgg aacagcaata ttagcccttc tcccgtaaga aaatcagtaa
+     2881 caccatcacc atataacgta acgaagcatc gtaaccgcca cttacaaaat attcaagact
+     2941 ctcaaagcgg taaaaacgga atcactccca caacaatgtc aacttcatct tctgacgatt
+     3001 ttgttccggt taaagatggt gaaaattttt gctgggtcca tagcatggaa ccagacagaa
+     3061 gaccaagtaa gaaaaggtta gtagattttt caaataagag taatgtcaat gttggtcaag
+     3121 ttaaggacat tcacggacgc atcccagaaa tgctgtgatt atacgcaacg atattttgct
+     3181 taattttatt ttcctgtttt attttttatt agtggtttac agatacccta tattttattt
+     3241 agtttttata cttagagaca tttaatttta attccattct tcaaatttca tttttgcact
+     3301 taaaacaaag atccaaaaat gctctcgccc tcttcatatt gagaatacac tccattcaaa
+     3361 attttgtcgt caccgctgat taatttttca ctaaactgat gaataatcaa aggccccacg
+     3421 tcagaaccga ctaaagaagt gagttttatt ttaggaggtt gaaaaccatt attgtctggt
+     3481 aaattttcat cttcttgaca tttaacccag tttgaatccc tttcaatttc tgctttttcc
+     3541 tccaaactat cgaccctcct gtttctgtcc aacttatgtc ctagttccaa ttcgatcgca
+     3601 ttaataactg cttcaaatgt tattgtgtca tcgttgactt taggtaattt ctccaaatgc
+     3661 ataatcaaac tatttaagga agatcggaat tcgtcgaaca cttcagtttc cgtaatgatc
+     3721 tgatcgtctt tatccacatg ttgtaattca ctaaaatcta aaacgtattt ttcaatgcat
+     3781 aaatcgttct ttttattaat aatgcagatg gaaaatctgt aaacgtgcgt taatttagaa
+     3841 agaacatcca gtataagttc ttctatatag tcaattaaag caggatgcct attaatggga
+     3901 acgaactgcg gcaagttgaa tgactggtaa gtagtgtagt cgaatgactg aggtgggtat
+     3961 acatttctat aaaataaaat caaattaatg tagcatttta agtataccct cagccacttc
+     4021 tctacccatc tattcataaa gctgacgcaa cgattactat tttttttttc ttcttggatc
+     4081 tcagtcgtcg caaaaacgta taccttcttt ttccgacctt ttttttagct ttctggaaaa
+     4141 gtttatatta gttaaacagg gtctagtctt agtgtgaaag ctagtggttt cgattgactg
+     4201 atattaagaa agtggaaatt aaattagtag tgtagacgta tatgcatatg tatttctcgc
+     4261 ctgtttatgt ttctacgtac ttttgattta tagcaagggg aaaagaaata catactattt
+     4321 tttggtaaag gtgaaagcat aatgtaaaag ctagaataaa atggacgaaa taaagagagg
+     4381 cttagttcat cttttttcca aaaagcaccc aatgataata actaaaatga aaaggatttg
+     4441 ccatctgtca gcaacatcag ttgtgtgagc aataataaaa tcatcacctc cgttgccttt
+     4501 agcgcgtttg tcgtttgtat cttccgtaat tttagtctta tcaatgggaa tcataaattt
+     4561 tccaatgaat tagcaatttc gtccaattct ttttgagctt cttcatattt gctttggaat
+     4621 tcttcgcact tcttttccca ttcatctctt tcttcttcca aagcaacgat ccttctaccc
+     4681 atttgctcag agttcaaatc ggcctctttc agtttatcca ttgcttcctt cagtttggct
+     4741 tcactgtctt ctagctgttg ttctagatcc tggtttttct tggtgtagtt ctcattatta
+     4801 gatctcaagt tattggagtc ttcagccaat tgctttgtat cagacaattg actctctaac
+     4861 ttctccactt cactgtcgag ttgctcgttt ttagcggaca aagatttaat ctcgttttct
+     4921 ttttcagtgt tagattgctc taattctttg agctgttctc tcagctcctc atatttttct
+     4981 tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgatc
+//